Merge pull request #69 from rki-mf1/release_v0.5

Release v0.5

CHANGELOG.md

@@ -5,6 +5,34 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.5.0] 2024-03-13
+
+### Changed
+
+- updated default `nextclade` version to `3.3.1`
+  - default dataset version `2024-02-16--04-00-32Z`
+- updated default `pangolin` version to `4.3`
+  - default `pangolin-data` version 1.25.1
+
+## [0.4.3] 2023-06-26
+
+### Fixed
+
+- fixed conda channel order
+- enhanced nextclade dataset provenance
+
+## [0.4.2] 2023-06-08
+
+### Added
+
+- added a DOI
+
+## [0.4.1] 2023-05-23
+
+### Changed
+
+- update documentation
+
 ## [0.4.0] 2023-05-09
 
 ### Added

CoVpipe2.nf

@@ -172,8 +172,8 @@ if ( workflow.containerEngine && params.update ) {
         params.pangolin_docker = "rkimf1/pangolin:" + tagname
         println "\033[0;32mFound latest pangolin container, using: " + params.pangolin_docker + " \033[0m" 
 
-        tagname = 'https://registry.hub.docker.com/v2/repositories/rkimf1/nextclade2/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
-        params.nextclade_docker = "rkimf1/nextclade2:" + tagname 
+        tagname = 'https://registry.hub.docker.com/v2/repositories/rkimf1/nextclade3/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
+        params.nextclade_docker = "rkimf1/nextclade3:" + tagname 
         println "\033[0;32mFound latest nextclade container, using: " + params.nextclade_docker + " \033[0m"
     } 
     if ( internetcheck.toString() == "false" ) { 

modules/nextclade.nf

@@ -25,7 +25,7 @@ process nextclade {
     cat tmp.tsv | tr -d "\r" > ${name}_clade.tsv
 
     used_nextclade_version=\$nextclade_version_curr
-    used_nextcladedataset_tag=\$(grep -Po '"tag":.*' data/${nextclade_dataset_name}/tag.json | cut -d' ' -f 2 | tr -d '"')
+    used_nextcladedataset_tag=\$(grep -Po '"tag":.*' data/${nextclade_dataset_name}/pathogen.json | cut -d' ' -f 2 | tr -d '"' | tr -d ',')
     used_nextcladedataset_info="${nextclade_dataset_name}, \$used_nextcladedataset_tag"
     """
     stub:

nextflow.config

@@ -74,12 +74,12 @@ params {
     // update settings and default container
     update = false
 
-    pangolin_docker_default = 'rkimf1/pangolin:4.2-1.18.1.1--e24af6d'
-    nextclade_docker_default = 'rkimf1/nextclade2:2.13.1--ddb9e60'
-    pangolin_conda_default = 'bioconda::pangolin=4.2 bioconda::pangolin-data=1.18.1.1'
-    nextclade_conda_default = 'bioconda::nextclade=2.13.1'
+    pangolin_docker_default = 'rkimf1/pangolin:4.3-1.25.1--380d5e9'
+    nextclade_docker_default = 'rkimf1/nextclade3:3.3.1--c7323e6'
+    pangolin_conda_default = 'bioconda::pangolin=4.3 bioconda::pangolin-data=1.25.1'
+    nextclade_conda_default = 'bioconda::nextclade=3.3.1'
     nextclade_dataset_name = 'sars-cov-2'
-    nextclade_dataset_tag = '2023-04-18T12:00:00Z'
+    nextclade_dataset_tag = '2024-02-16--04-00-32Z'
 
     // output folder structure
     output = 'results'

tests/test.yml

@@ -100,14 +100,14 @@
     - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE.aligned.fasta"
       md5sum: 59ee3f944dcda28f16c20f00a819aa0e
     - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_clade.tsv"
-      md5sum: 6cdd6ae28611b295d06594993f8ab3bc
+      md5sum: 92f74146db907b4c8086ccbb550953c8
     - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_lineage_report.csv"
       contains:
         - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note"
     - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE.aligned.fasta"
       md5sum: e1936924ec8fe26dbc87a2277e4a3dac
     - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_clade.tsv"
-      md5sum: ac2e403922170a07a41a48947b768a12
+      md5sum: aa9ff26b8308444690ce986dfe7bed59
     - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_lineage_report.csv"
       contains:
         - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note"
@@ -127,9 +127,9 @@
       md5sum: b649f9400fe6842b2f8a2537e137f66a
     - path: "results/Report/report_datatable.xlsx"
     - path: "results/Report/single_tables/nextclade_results.tsv"
-      md5sum: 58b42101676f5fab5d82c94b8dd91671
+      md5sum: 7823b5b56e31a5412263384f10d7f204
     - path: "results/Report/single_tables/pangolin_results.csv"
-      md5sum: df49cfb48015c8df2ce402aac0ce7a98
+      md5sum: fcf7e3bc0b3c852a08a8ba801c406920
     - path: "results/Report/single_tables/president_results.tsv"
     - path: "results/Report/single_tables/sc2rf_results.csv"
       md5sum: d02d8ab1b54d11b1aa16edc719b75796
@@ -236,14 +236,14 @@
     - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE.aligned.fasta"
       md5sum: 59ee3f944dcda28f16c20f00a819aa0e
     - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_clade.tsv"
-      md5sum: a4ac4a5a69067232f1d9919a45f9ecab
+      md5sum: 92f74146db907b4c8086ccbb550953c8
     - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_lineage_report.csv"
       contains:
         - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note"
     - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE.aligned.fasta"
       md5sum: e1936924ec8fe26dbc87a2277e4a3dac
     - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_clade.tsv"
-      md5sum: a8bd3d4e09ae750f07ae6cd5d8a83def
+      md5sum: aa9ff26b8308444690ce986dfe7bed59
     - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_lineage_report.csv"
       contains:
         - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note"
@@ -263,7 +263,7 @@
       md5sum: b649f9400fe6842b2f8a2537e137f66a
     - path: "results/Report/report_datatable.xlsx"
     - path: "results/Report/single_tables/nextclade_results.tsv"
-      md5sum: dc7a07bc062837349d151c8946ae29c2
+      md5sum: 7823b5b56e31a5412263384f10d7f204
     - path: "results/Report/single_tables/pangolin_results.csv"
     - path: "results/Report/single_tables/president_results.tsv"
     - path: "results/Report/single_tables/sc2rf_results.csv"